Comparative and demographic analysis of orang-utan genomes

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Devin P. Locke, The Genome Center at Washington University, Washington University School of Medicine, United States
  • LaDeana W. Hillier, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Wesley C. Warren, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Shiaw-Pyng Yang, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Zhengyuan Wang, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Asif T. Chinwalla, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Pat Minx, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Makedonka Mitreva, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Lisa Cook, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Kim D. Delehaunty, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Catrina Fronick, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Heather Schmidt, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Lucinda A. Fulton, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Robert S. Fulton, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Joanne O. Nelson, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Vincent Magrini, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Craig Pohl, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Tina A. Graves, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Chris Markovic, The Genome Center at Washington University, Washington University School of Medicine, United States
  • George M. Weinstock, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Elaine R. Mardis, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Richard K. Wilson, The Genome Center at Washington University, Washington University School of Medicine, United States
  • Kim C. Worley, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Lynne V. Nazareth, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Donna M. Muzny, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Andy Cree, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Huyen H. Dinh, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Jennifer Hume, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Christie L. Kovar, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Gerald R. Fowler, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Jeffrey Rogers, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Richard A. Gibbs, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, United States
  • Gerton Lunter, MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom
  • Stephen Meader, MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom
  • Andreas Heger, MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom
  • Chris P. Ponting, MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom
  • Tomas Marques-Bonet, Department of Genome Sciences, University of Washington School of Medicine, United States
  • Can Alkan, Department of Genome Sciences, University of Washington School of Medicine, United States
  • Lin Cheng, Department of Genome Sciences, University of Washington School of Medicine, United States
  • Ze Cheng, Department of Genome Sciences, University of Washington School of Medicine, United States
  • Jeffrey M. Kidd, Department of Genome Sciences, University of Washington School of Medicine, United States
  • Evan E. Eichler, Department of Genome Sciences, University of Washington School of Medicine, United States
  • Rui Faria, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Olga Fernando, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Fleur Darré, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Domèmec Farré, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Elodie Gazave, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Meritxell Oliva, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Arcadi Navarro, IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Spain
  • Simon White, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom
  • Stephen Searle, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom
  • Albert J. Vilella, European Bioinformatics Institute, Wellcome Trust Genome Campus, United Kingdom
  • Yuan Chen, European Bioinformatics Institute, Wellcome Trust Genome Campus, United Kingdom
  • Paul Flicek, European Bioinformatics Institute, Wellcome Trust Genome Campus, United Kingdom
  • Javier Herrero, European Bioinformatics Institute, Wellcome Trust Genome Campus, United Kingdom
  • Jian Ma, Center for Biomolecular Science and Engineering, University of California, United States
  • Brian Raney, Center for Biomolecular Science and Engineering, University of California, United States
  • Bernard Suh, Center for Biomolecular Science and Engineering, University of California, United States
  • David Haussler, Center for Biomolecular Science and Engineering, University of California, United States
  • Richard Burhans, Center for Comparative Genomics and Bioinformatics, Penn State University, United States
  • Aakrosh Ratan, Center for Comparative Genomics and Bioinformatics, Penn State University, United States
  • Robert S. Harris, Center for Comparative Genomics and Bioinformatics, Penn State University, United States
  • Webb Miller, Center for Comparative Genomics and Bioinformatics, Penn State University, United States
  • Roberta Roberto, Department of Biology, University of Bari, Italy
  • Oronzo Capozzi, Department of Biology, University of Bari, Italy
  • Nicoletta Archidiacono, Department of Biology, University of Bari, Italy
  • Mariano Rocchi, Department of Biology, University of Bari, Italy
  • Giuliano Della Valle, Department of Biology, University of Bologna, Italy
  • Stefania Purgato, Department of Biology, University of Bologna, Italy
  • Miriam K. Konkel, Department of Biological Sciences, Louisiana State University, United States
  • Jerilyn A. Walker, Department of Biological Sciences, Louisiana State University, United States
  • Mark A. Batzer, Department of Biological Sciences, Louisiana State University, United States
  • Brygg Ullmer, Center for Computation and Technology, Department of Computer Sciences, Louisiana State University, United States
  • Adrian F. A. Smit, Institute for Systems Biology, Seattle, United States
  • Robert Hubley, Institute for Systems Biology, Seattle, United States
  • Claudio Casola, Department of Biology and School of Informatics and Computing, Indiana University, United States
  • Daniel R. Schrider, Department of Biology and School of Informatics and Computing, Indiana University, United States
  • Matthew W. Hahn, Department of Biology and School of Informatics and Computing, Indiana University, United States
  • Victor Quesada, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spain
  • Xose S. Puente, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spain
  • Gonzalo R. Ordoñez, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spain
  • Carlos López-Otín, Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Spain
  • Tomas Vinar, Faculty of Mathematics, Physics and Informatics, Comenius University, Slovakia
  • Brona Brejova, Faculty of Mathematics, Physics and Informatics, Comenius University, Slovakia
  • Carolin Kosiol, Institut für Populations genetik, Vetmeduni Vienna, Austria
  • Heather A. Lawson, Department of Anatomy and Neurobiology, Washington University School of Medicine, United States
  • Vikas Taliwal, Department of Biological Statistics and Computational Biology, Cornell University, United States
  • André L. Martins, Department of Biological Statistics and Computational Biology, Cornell University, United States
  • Adam Siepel, Department of Biological Statistics and Computational Biology, Cornell University, United States
  • Xin Ma, Department of Biological Statistics and Computational Biology, Cornell University, United States
  • Jeremiah Degenhardt, Department of Biological Statistics and Computational Biology, Cornell University, United States
  • Arindam RoyChoudhury, Department of Biostatistics, Columbia University, United States
  • Carlos D. Bustamante, Department of Genetics, Stanford University, United States
  • Ryan N. Gutenkunst, Department of Molecular and Cellular Biology, University of Arizona, United States
  • Thomas Mailund
  • Julien Dutheil, Denmark
  • Asger Hobolth
  • Mikkel Heide Schierup
  • Oliver A. Ryder, San Diego Zoo's Institute for Conservation Research, United States
  • Yuko Yoshinaga, Children’s Hospital Oakland Research Institute, United States
  • Pieter J. de Jong, Children’s Hospital Oakland Research Institute, United States
‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
Original languageEnglish
JournalNature
Volume469
Pages (from-to)529-533
Number of pages5
ISSN0028-0836
DOIs
Publication statusPublished - 2011

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